Has science disproved the miracles associated with Jesus Christ?

No. Science depends upon observation and replication. Miracles, such as the Incarnation (Christ's virgin birth) and the Resurrection, are by their very nature unprecedented events. No one can replicate these events in a laboratory. Hence, science simply cannot be the judge and jury as to whether or not these events occurred.

The scientific method is useful for studying nature but not super-nature. Just as football stars are speaking outside their field of expertise when they appear on television to tell you what razor you should buy, so scientists are speaking outside their field when they address theological issues like miracles or the Resurrection.

MANY WITNESSES WERE STILL ALIVE WHEN THE RECORD WAS PUBLISHED. One highly pertinent factor is the brief time that elapsed between Jesus' miraculous public ministry and the publication of the gospels. It was insufficient for the development of miracle legends. Many eyewitnesses to Jesus' miracles would have still been alive to refute any untrue miracle accounts (see 1 Corinthians 15:6).

MEN OF NOBLE CHARACTER. One must also recognize the noble character of the men who witnessed these miracles (Peter, James, and John, for example). Such men were not prone to misrepresentation, and were willing to give up their lives rather than deny their beliefs.

HOSTILE WITNESSES PROVIDED NO DISPUTE. There were also hostile witnesses to the miracles of Christ. When Jesus raised Lazarus from the dead, for example, none of the chief priests or Pharisees disputed the miracle (John 11:45-48). (If they could have disputed it, they would have.) Rather, their goal was simply to stop Jesus (verses 47-48). Because there were so many hostile witnesses who observed and scrutinized Christ, successful “fabrication” of miracle stories in His ministry would have been impossible.

Science, Nature and Scripture

I believe that nature and Scripture, properly interpreted, do not conflict. God has communicated to humankind both by general revelation (nature, or the observable universe) and special revelation (the Bible). Since both of these revelations come from God—and since God does not contradict Himself—we must conclude that these two revelations are in agreement with each other. While there may be conflicts between one's interpretation of the observable universe and one's interpretation of the Bible, there is no ultimate contradiction.

We might say that science is a fallible human interpretation of the observable universe while theology is a fallible human interpretation of the Scriptures. If the secularist challenges the idea that science can be fallible, remind him or her of what science historian Thomas Kuhn proved in his book The Structure of Scientific Revolutions—that is, science is in a constant state of change. New discoveries have consistently caused old scientific paradigms to be discarded in favor of newer paradigms.

Here is the point:

It is not nature and Scripture that contradict; rather, it is science (man's fallible interpretation of nature) and theology (man's fallible interpretation of Scripture) that sometimes fall into conflict. Hence the secularist cannot simply dismiss certain parts of the Bible because “science and the Bible contradict.”